started on tables

latex/tex/kapitel/abkuerzungen.tex

@@ -15,6 +15,7 @@
   \acro{FASTQ}{File Format Based on FASTA}
   \acro{FTP}{File Transfere Protocol}
   \acro{GA4GH}{Global Alliance for Genomics and Health}
+  \acro{GECO}{Genome Compressor}
   \acro{IUPAC}{International Union of Pure and Applied Chemistry}
   \acro{LZ77}{Lempel Ziv 1977}
   \acro{LZ78}{Lempel Ziv 1978}

latex/tex/kapitel/k6_results.tex

@@ -6,15 +6,98 @@
 
 \chapter{Results and Discussion}
 
-\begin{tabular}{ |p{3cm}||p{3cm}|p{3cm}|  }
+\begin{table}[ht]
+\caption{Multi-column table}
+\begin{center}
+\begin{tabular}{cc}
+    \hline
+    \multicolumn{2}{c}{Multi-column}\\
+    X&X\\
+    \hline
+\end{tabular}
+\end{center}
+\label{tab:multicol}
+\end{table}
+
+
+\begin{table}[ht]
+\caption{Multi-column table}
+\begin{center}
+\begin{tabular}{ |p{3cm}||p{3cm}|p{3cm}|p{3cm}| }
+ \hline
+ \multicolumn{4}{|c|}{ratio}\\
+ \hline
+ h: tool v: taks&GeCo&samtools to BAM& samtools to CRAM\\
  \hline
- \multicolumn{4}{|c|}{Overall time and compression ratio sorted by tools} \\
+  method/taks& geco &sam -> bam &sam -> cram\\
+%  conversion& - &- & \\
+%  compression in ms& & & \\
+%  compression ratio& & & \\
+ \hline
+\end{tabular}
+\end{center}
+\label{tab:multicol}
+\end{table}
+
+
+\begin{tabular}{ |p{3cm}||p{3cm}|p{3cm}|p{3cm}|  }
  \hline
- horizontal: tool, vertical: taks& \ac{GeCo}& Samtools& Samtools CRAM\\
+ \multicolumn{4}{|c|}{Compression time} \\
+ \hline
+   & \acs{GECO}& Samtools&\\
  \hline
  % method/taks& geco &sam -> bam &sam -> cram\\
-  conversion& - & & 
-  compression in ms& & & 
-  compression ratio& & & 
+ File 1 & 235005& 15178&  \\
+ File 2 & 246503& 15211&  \\
+ File 3 & 20169& 12526&  \\
+ File 4 & 194081& 11986&  \\
+ File 5 & 183878& 11436&  \\
+ File 6 & 173646& 10738&  \\
+ File 7 & 159999& 9995&  \\
+ File 8 & 148288& 9142&  \\
+ File 9 & 12304& 8276&  \\
+ File 10 & 134937& 8460&  \\
+ File 11 & 136299& 8508&  \\
+ File 12 & 134932& 8467&  \\
+ File 13 & 999022& 6770&  \\
+ File 14 & 924753& 6309&  \\
+ File 15 & 852555& 5959&  \\
+ File 16 & 827651& 5481&  \\
+ File 17 & 820814& 5151&  \\
+ File 18 & 798429& 5012&  \\
+ File 19 & 586058& 3662&  \\
+ File 20 & 645884& 4025&  \\
+ File 21 & 411984& 2783&  \\
+ \hline
+\end{tabular}
+
+
+\begin{tabular}{ |p{3cm}||p{3cm}|p{3cm}|p{3cm}|  }
+ \hline
+ \multicolumn{4}{|c|}{File sizes} \\
+ \hline
+   & Source file& \acs{GECO}& Samtools CRAM\\
+ \hline
+  File 1& 253105752& 46364770& 55769827\\
+  File 2& 136027438& 27411806& 32238052\\
+  File 3& 137338124& 27408185& 32529673\\
+  File 4& 135496623& 27231126& 32166751\\
+  File 5& 116270459& 20696778& 23568321\\
+  File 6& 108827838& 18676723& 21887811\\
+  File 7& 103691101& 16804782& 20493276\\
+  File 8& 91844042& 16005173& 19895937\\
+  File 9& 84645123& 15877526& 20177456\\
+  File 10& 81712897& 16344067& 19310998\\
+  File 11& 59594634& 10488207& 14251243\\
+  File 12& 246230144& 49938168& 58026123\\
+  File 13& 65518294& 13074402& 15510100\\
+  File 14& 47488540& 7900773& 9708258\\
+  File 15& 51665500& 41117340& 47707954\\
+  File 16& 201600541& 39248276& 45564837\\
+  File 17& 193384854& 37133480& 43655371\\
+  File 18& 184563953& 35355184& 40980906\\
+  File 19& 173652802& 31813760& 38417108\\
+  File 20& 162001796& 30104816& 34926945\\
+  File 21& 147557670& 23932541& 29459829\\
  \hline
 \end{tabular}

latex/tex/preambel.tex

@@ -18,6 +18,7 @@
 \usepackage{graphicx}             % Bilder einbinden
 \usepackage{enumitem}             % Eigene Listen definieren können
 \usepackage{setspace}             % Abstände korrigieren
+\usepackage{multirow}
 
 % Setzen von Optionen abhängig von der gewählten Sprache. Die Sprache wird
 % in thesis.tex gesetzt.

results/size_calc/add.py

@@ -0,0 +1,33 @@
+# for kb, mb divide by 1024, 1049000
+
+
+src = []
+with open('src.txt') as f:
+ src = f.readlines()
+
+geco = []
+with open('geco.txt') as f:
+  geco = f.readlines()
+
+cram = []
+with open('cram.txt') as f:
+  cram = f.readlines()
+
+i=0
+while i < len(src):
+  s = int(src[i])
+  g = int(geco[i])
+  c = int(cram[i])
+  print(f"File {i+1}& {s}& {g}& {c}")
+  #print(f"Homo\_sapiens.GRCh38.dna.chromosome.{i+1}& {s}& {g}& {c}")
+  i = i + 1
+
+"""
+  s = int(src[i])
+  g = int(geco[i])
+  c = int(cram[i])
+
+  s = int(src[i].replace('\n', ''))
+  g = int(geco[i].replace('\n', ''))
+  c = int(cram[i].replace('\n', ''))
+"""

results/size_calc/add_sam.py

@@ -0,0 +1,38 @@
+# for kb, mb divide by 1024, 1049000
+
+
+sam = []
+with open('sam.txt') as f:
+ sam = f.readlines()
+
+bam = []
+with open('bam.txt') as f:
+  bam = f.readlines()
+
+cram = []
+with open('cram.txt') as f:
+  cram = f.readlines()
+
+"""
+   & Source File&SAM &BAM %CRAM\\
+ \hline
+
+"""
+i=0
+while i < len(sam):
+  s = int(sam[i])
+  g = int(bam[i])
+  c = int(cram[i])
+  print(f"File {i+1}& {s}& {g}& {c}")
+  #print(f"Homo\_sapiens.GRCh38.dna.chromosome.{i+1}& {s}& {g}& {c}")
+  i = i + 1
+
+"""
+  s = int(sam[i])
+  g = int(bam[i])
+  c = int(cram[i])
+
+  s = int(sam[i].replace('\n', ''))
+  g = int(bam[i].replace('\n', ''))
+  c = int(cram[i].replace('\n', ''))
+"""

results/size_calc/bam.txt

@@ -0,0 +1,21 @@
+62048289
+35855955
+35894133
+35580843
+26467775
+24284901
+22486646
+21568790
+21294270
+20684650
+14616042
+65391181
+16769658
+10477999
+53586949
+51457814
+48838053
+46216304
+42371043
+39107538
+32708272

results/size_calc/cram.txt

@@ -0,0 +1,21 @@
+55769827
+32238052
+32529673
+32166751
+23568321
+21887811
+20493276
+19895937
+20177456
+19310998
+14251243
+58026123
+15510100
+9708258
+47707954
+45564837
+43655371
+40980906
+38417108
+34926945
+29459829

results/size_calc/geco.txt

@@ -0,0 +1,21 @@
+46364770
+27411806
+27408185
+27231126
+20696778
+18676723
+16804782
+16005173
+15877526
+16344067
+10488207
+49938168
+13074402
+7900773
+41117340
+39248276
+37133480
+35355184
+31813760
+30104816
+23932541

results/size_calc/sam.txt

@@ -0,0 +1,21 @@
+248956528
+133797529
+135086729
+133275416
+114364435
+107043825
+101991296
+90338452
+83257548
+80373392
+58617723
+242193635
+64444274
+46710090
+198295665
+190214661
+181538365
+170806085
+159346079
+145138742
+138394823

results/size_calc/src.txt

@@ -0,0 +1,22 @@
+253105752
+136027438
+137338124
+135496623
+116270459
+108827838
+103691101
+91844042
+84645123
+81712897
+59594634
+246230144
+65518294
+47488540
+51665500
+201600541
+193384854
+184563953
+173652802
+162001796
+147557670
+140701352